Matteo Costacurta
- Total activity 9
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 4
Activity overview
Latest activity by Matteo Costacurta-
Matteo Costacurta commented,
Hi James, I had to re-download all the files from the bucket. I decompressed with bcftools, indexed with IndexFeatureFile and they all validated with ValidateVariants, except resources_broad_hg38...
-
Matteo Costacurta commented,
Hi Genevieve, I am experiencing the same problem while trying to use BaseRecalibrator. Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM he...
-
Matteo Costacurta commented,
Hi ISmolicz, Those two options successfully forced the calling of all the variants in my bam files, so that worked fine for me. I am using GATK 4.3.0.0. Without those options, Mutect2 would just ig...
-
Matteo Costacurta created a post,
Error loading filtermutectcalls.var.vcf.gz in IGV 2.16.0 - htsjdk.samtools.util.RuntimeIOException [file] has invalid uncompressedLength
Hello GATK team, I have called variants with Mutect2 and filtered with FilterMutectCalls, generating a final vcf.gz file. When I upload this file in IGV I get this error: I have tried to view it w...
-
Matteo Costacurta commented,
Hello GATK team, I am currently experiencing similar issues with calling variants from some genes with possibly some complexity, such as FLG, with Mutect2 (versions 4.1.2.0, 4.2.2.0 and 4.3.0.0) no...